17004: Setting intermediate collection fields

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index 7964486ff25b2584af54ef84da8b4327207daabb..0b8f2ca707bda7e58da8cfc306f071ed13ac980b 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -146,6 +146,8 @@ class ArvadosContainer(JobBase):
                     mounts[targetdir]["path"] = path
             prevdir = targetdir + "/"
 
+        intermediate_collection_info = arvados_cwl.util.get_intermediate_collection_info(self.name, runtimeContext.current_container, runtimeContext.intermediate_output_ttl)
+
         with Perf(metrics, "generatefiles %s" % self.name):
             if self.generatefiles["listing"]:
                 vwd = arvados.collection.Collection(api_client=self.arvrunner.api,
@@ -197,12 +199,11 @@ class ArvadosContainer(JobBase):
 
                 if not runtimeContext.current_container:
                     runtimeContext.current_container = arvados_cwl.util.get_current_container(self.arvrunner.api, self.arvrunner.num_retries, logger)
-                info = arvados_cwl.util.get_intermediate_collection_info(self.name, runtimeContext.current_container, runtimeContext.intermediate_output_ttl)
                 vwd.save_new(name=info["name"],
                              owner_uuid=runtimeContext.project_uuid,
                              ensure_unique_name=True,
-                             trash_at=info["trash_at"],
-                             properties=info["properties"])
+                             trash_at=intermediate_collection_info["trash_at"],
+                             properties=intermediate_collection_info["properties"])
 
                 prev = None
                 for f, p in sorteditems:
@@ -346,6 +347,8 @@ class ArvadosContainer(JobBase):
             for pr in output_properties_req["processProperties"]:
                 container_request["output_properties"][pr["propertyName"]] = self.builder.do_eval(pr["propertyValue"])
 
+        output_properties.update(intermediate_collection_info["properties"])
+
         if runtimeContext.runnerjob.startswith("arvwf:"):
             wfuuid = runtimeContext.runnerjob[6:runtimeContext.runnerjob.index("#")]
             wfrecord = self.arvrunner.api.workflows().get(uuid=wfuuid).execute(num_retries=self.arvrunner.num_retries)